Transcriptome analyses reveal molecular mechanisms underlying functional recovery after spinal cord injury

Proc Natl Acad Sci U S A. 2015 Oct 27;112(43):13360-5. doi: 10.1073/pnas.1510176112. Epub 2015 Oct 12.


Spinal cord injury (SCI) is considered incurable because axonal regeneration in the central nervous system (CNS) is extremely challenging, due to harsh CNS injury environment and weak intrinsic regeneration capability of CNS neurons. We discovered that neurotrophin-3 (NT3)-loaded chitosan provided an excellent microenvironment to facilitate nerve growth, new neurogenesis, and functional recovery of completely transected spinal cord in rats. To acquire mechanistic insight, we conducted a series of comprehensive transcriptome analyses of spinal cord segments at the lesion site, as well as regions immediately rostral and caudal to the lesion, over a period of 90 days after SCI. Using weighted gene coexpression network analysis (WGCNA), we established gene modules/programs corresponding to various pathological events at different times after SCI. These objective measures of gene module expression also revealed that enhanced new neurogenesis and angiogenesis, and reduced inflammatory responses were keys to conferring the effect of NT3-chitosan on regeneration.

Keywords: NT3; WGCNA; chitosan; spinal cord injury; transcriptome.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Cellular Microenvironment / physiology*
  • Chitosan / therapeutic use
  • Computational Biology / methods
  • Enzyme-Linked Immunosorbent Assay
  • Gene Expression Profiling / methods
  • Microarray Analysis
  • Neovascularization, Physiologic / physiology
  • Neurogenesis / physiology
  • Neurotrophin 3 / pharmacology*
  • Neurotrophin 3 / therapeutic use
  • Polymerase Chain Reaction
  • Rats
  • Rats, Wistar
  • Recovery of Function / drug effects
  • Recovery of Function / genetics
  • Recovery of Function / physiology*
  • Spinal Cord Injuries / genetics
  • Spinal Cord Injuries / metabolism*


  • Neurotrophin 3
  • Chitosan

Associated data

  • GEO/GSE69334